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def _run_region(bam, region, *args, **kwargs):
data_gen = medaka.features.SampleGenerator(
bam, region, *args, **kwargs)
return data_gen.samples, data_gen._quarantined
def sample_gen():
# chain all samples whilst dispensing with generators when done
# (they hold the feature vector in memory until they die)
for region in regions:
data_gen = medaka.features.SampleGenerator(
bam, region, model_file, rle_ref, read_fraction,
chunk_len=chunk_len, chunk_overlap=chunk_ovlp,
tag_name=tag_name, tag_value=tag_value,
tag_keep_missing=tag_keep_missing,
enable_chunking=enable_chunking)
yield from data_gen.samples
remainder_regions.extend(data_gen._quarantined)
batches = medaka.common.background_generator(
def _samples_worker(args, region, feature_encoder, label_scheme):
logger = medaka.common.get_named_logger('PrepWork')
logger.info("Processing region {}.".format(region))
data_gen = SampleGenerator(
args.bam, region, feature_encoder, truth_bam=args.truth,
label_scheme=label_scheme, truth_haplotag=args.truth_haplotag,
chunk_len=args.chunk_len, chunk_overlap=args.chunk_ovlp)
return list(data_gen.samples), region